A government vet has been removed after exposing the appalling conditions on live cattle export ships 

LEIGH SALES, PRESENTER: More shocks from inside our $2 billion live cattle export industry.

A respected vet has been removed from her government role after she wrote a no holds barred report revealing the suffering of animals on board live export ships.

7.30 has obtained footage never before seen publicly along with evidence that the Government was willing to sacrifice the vet in response to industry pressure.

James Thomas has this investigation, and a warning: some viewers might find images in this report distressing.

LYNN SIMPSON, FMR LIVE EXPORT VETERINARIAN: This industry entails unnecessary pain and suffering for the animals and I would say anyone who tells you any different is either a liar, they're ill-informed or they're staying silent because they're in fear of losing their job.

JAMES THOMAS, REPORTER: Dr Lynn Simpson was one of Australia's most experienced and respected live export veterinarians. She sailed 57 voyages, worked for every exporter in the country and consulted widely to industry.

LYNN SIMPSON: I was legally mandated to monitor and report conditions that I was seeing for animal health and welfare on these ships.

JAMES THOMAS: But from her first voyage, she had concerns about the treatment of animals on board the live export ships.

LYNN SIMPSON: These are all my images of what I've seen in live export vessels. They're not sanitised, they show animals in appalling conditions, there's pain, there's suffering, it's inexcusable and it's confronting.

JAMES THOMAS: Rivers of faeces contaminate drinking water and food troughs. Beasts covered in excrement suffocate or die of heat exhaustion. And inadequate bedding causes injuries which can lead to euthanasia. All of these images were taken on board live export ships approved as compliant to today's Australian standards.

LYNN SIMPSON: Well, it's just business as usual on these ships. I expect to see leg injuries, I expect to see pneumonia, I expect to see animals drenched in faecal matter.

JAMES THOMAS: After lodging complaints with exporters to no avail for more than a decade, Dr Simpson left the live export ships to join the government regulator in 2012.

LYNN SIMPSON: And so I contacted the Department of Agriculture and they said, "Well actually, we're about to start the review of the Australian standards for exporting livestock, which we call ASEL, and you would be the perfect technical advisor for it."

JAMES THOMAS: Dr Simpson's damning images formed the basis of a report that she was asked to submit to the Government's review of standards. It was explosive and unprecedented.

BIDDA JONES, CHIEF SCIENTIST, RSPCA: My response when I saw Lynn's photographs was, "That's what it's like? Like, that's really what it's like?" Just shocked.

JAMES THOMAS: The RSPCA's chief scientist, Bidda Jones, was a member of the government review that received Dr Simpson's report. She was used to seeing images of the ships supplied by the industry that looked like this:

FEMALE VOICEOVER (Nighty Ships): One of the stockman's biggest jobs is just keeping their cattle calm.

JAMES THOMAS: Now, she and other members of the review panel were seeing images like this.

BIDDA JONES: This was the first time that an on board vet had actually produced a report on conditions on board with photographs.

JAMES THOMAS: An internal departmental minute obtained by the ABC clearly states that Dr Simpson's submission was, "not to be made publicly available," but it was.

LYNN SIMPSON: I knew immediately that that meant my career was over.

JAMES THOMAS: Someone at the department accidentally uploaded the report to the department's website - an administrative error that would change Dr Simpson's life forever.

BIDDA JONES: I walked into a committee meeting one day and she wasn't there and that was after her submission had been uploaded and made public. I mean, the only explanation that I could think of was that someone didn't like the fact that her photographs, her submission, her description of conditions on board vessels had been put out there into the public so those photographs were now out there for everybody to see.

LYNN SIMPSON: When they finally pulled me into the deputy secretary's office and said, "You can't be part of this anymore, industry ...," - and their words were, "Industry has a witch-hunt against you."

JAMES THOMAS: The ABC has obtained a letter from one of Dr Simpson's bosses, a senior executive with the department, Karen Schneider. It supports the claim that the Government did remove Dr Simpson because of pressure from the live export industry. Ms Schneider writes that Dr Simpson can no longer, "... continue working in the Animal Welfare Branch," because, "... the industry with which we engage has expressed the view that they cannot work with you."

Ms Schneider's letter then makes a stunning admission. She says, "I would like to stress that I do not share the expressed views of industry." And, "... your technical expertise is valued by the Department."

LYNN SIMPSON: She basically said in the letter that, "You've done nothing wrong, but the industry essentially doesn't like you, so you can't be here anymore." End of story.

JAMES THOMAS: From that point, Dr Simpson's role with the government review panel and the Animal Welfare Branch was over.

LYNN SIMPSON: For the industry to be able to kick a government employee out of a government job, that speaks volumes. I mean, it's a form of corruption. And that's all there is to it.

JAMES THOMAS: Karen Schneider didn't return our calls and the Department of Agriculture says it doesn't generally comment on employment matters, leaving the industry to field questions on Dr Simpson's removal.

SIMON CREAN, AUST. LIVE EXPORTERS' COUNCIL CHAIRMAN: Anyone can talk about the past. We acknowledge that the past mistakes were made. The issue is: are we prepared to learn from the mistakes and improve them?

JAMES THOMAS: That was Simon Crean in an interview three weeks ago. As chairman of the Australian Livestock Exporters' Council, known as ALEC, he'd invited us to Darwin to witness improvements to animal welfare in the live export trade. But last week, 7.30 revealed this: the story which showed apparently Australian cattle being sledge hammered to death in Vietnam has left the live export industry reeling, and while they deny pressuring government to sack Dr Simpson, Mr Crean is now taking a more conciliatory tone.

SIMON CREAN: I accept the fact that Dr Lynn Simpson has felt aggrieved by the treatment that she got. If that's the case, then on behalf of ALEC, I apologise for it. What we are now proposing is that we more actively engage, openly engage the veterinary profession, have a workshop and we would be more than happy to invite Dr Lynn to participate in that workshop.

SUE FOSTER, ADJUNCT SENIOR LECTURER, MURDOCH UNI.: The stocking density on the ships are the same, the Australian standards for the export of livestock are the same, most of the ships are still the same and there's still no legal requirement for an independent veterinarian on those ships. Most of the ships travel without a veterinarian at all.

LYNN SIMPSON: They've got you over a barrel in a way because you're employed by them and if you say the wrong thing, then you won't get another job.

JAMES THOMAS: Dr Simpson used to think that she could make a difference from within the system. Now, she is taking the system to the Federal Court, suing the Commonwealth for breach of contract.

LYNN SIMPSON: I was definitely a clean player in a dirty game and I think it's disgusting that they've shut me down, having come up with such strong, sensible evidence regarding how we can improve this trade.

LEIGH SALES: James Thomas and that report was produced by Rebecca Armitage.